After a while, you'll have several annexes, with different file contents. You don't have to try to keep all that straight; git-annex does location tracking for you. If you ask it to get a file and the drive or file server is not accessible, it will let you know what it needs to get it:

$ git annex get video/
get video/ (not available)
  Unable to access these remotes: usbdrive, server
  Try making some of these repositories available:
    5863d8c0-d9a9-11df-adb2-af51e6559a49  -- my home file server
    58d84e8a-d9ae-11df-a1aa-ab9aa8c00826  -- portable USB drive
    ca20064c-dbb5-11df-b2fe-002170d25c55  -- backup SATA drive
$ sudo mount /media/usb
$ git annex get video/
get video/ (from usbdrive...) ok